You may manually change the pathway layout by activating the node-move and entry-editing - mode (button 2) in the button bar at the most left of the application window. Then click onto graph node and hold and move the mouse to change the position of a node. You may also move a number of nodes (first select multiple nodes with Ctrl+click or the node selection commands available in the “Edit” menu and the “Process” tab), with the same technique. There are some layout-command-buttons (for example align nodes vertically or horizontal) in the button bar at the top. You may also modify the node positions by defining the X or Y position in the “Node” tab and the there appearing X/Y node attribute values (click “Apply & Redraw at the bottom to apply the changes).

 

Editing of Entries

By clicking the “Update KGML model” button in the “Process” tab, the active graph editor window will be evaluated as a KGML model. Below the command button you get an overview of the model content (list of Entries, Relations and Reactions). By clicking onto a row in the list, the corresponding graph element is selected in the graph view.

You may directly edit all aspects of a entry (shown as a graph node in the view), by double-clicking a node. You may also select a single or a number of graph nodes (to do so, Ctrl+click the desired nodes or use any of the other selection command), and use the “Node” tab, to modify some of the entry properties (e.g. change the color of a single or multiple entries). Do not forget to click the “Apply & Redraw” button, after changing properties in the “Node” tab. Some entry properties, like the KEGG ID, may be changed only by double-click a graph node.

 

By double-clicking a graph-edge, you may edit relations or reactions, connected to the graph edge.

 

By deleting a graph node (select the desired nodes and choosing “Edit/Delete” or using the “Del”-key), the corresponding KGML entry (and “background-entries” of maplink-nodes) are removed from the underlying KGML model. Also relations, which are connected to the deleted entries will be removed. If the deleted entry is a substrate or product of a reaction, the substrate or product will be removed from the reaction definition.

You may also delete graph edges. In such a case all relations, connected to that edge will be removed from the KGML model. Reaction products or substrates may be removed from the reaction definition as well (if no other reaction definition in the graph defines the same product or substrate).

By double-clicking a graph edge, you may also delete a single relation or modify a reaction product, substrate or enzyme definition.

By double-clicking a maplink-node, you may also delete “background-entries”, which are not visible in the graph view, and which are connected to a particular maplink-node.

 

You may create new entries by enabling the node/edge-creation mode: click onto the first button in the button bar at the most left of the application window. Click at the point, where the new entry should be created. After definition of the entry properties (you may use the search option as described in the program dialog window to ease the creation of entries), the pathway view will be updated and will show the new entry.

To create “background-entries”, connected to a maplink-node, double-click a maplink-node and choose the option “Edit/Add (hidden) Entries”. Then select the checkbox “Add Background-Entry” in the second appearing dialog.

 

You may create new relations by enabling the node/edge-creation mode: click onto the first button in the button bar at the most left of the application window. You may then create new graph edges by clicking at a source graph node and then clicking onto a target graph node. By doing so, the source and target of a new relation is pre-defined. By choosing “Edit Relation(s)”, you may create and specify a new relation. For the definition of a reaction, choose “Edit Reactions”. While the created edge defines the initial source and target of a relation, a newly created reaction has no predefined settings. So the reaction substrates, enzymes and products need to be fully specified.